A comprehensive survey of integron-associated genes present in metagenomes
Background Integrons are genomic elements that mediate horizontal gene transfer by
inserting and removing genetic material using site-specific recombination. Integrons are …
inserting and removing genetic material using site-specific recombination. Integrons are …
Baseline human gut microbiota profile in healthy people and standard reporting template
CH King, H Desai, AC Sylvetsky, J LoTempio… - PloS one, 2019 - journals.plos.org
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy
human gut is necessary before any kind of pre-clinical or clinical study can be performed …
human gut is necessary before any kind of pre-clinical or clinical study can be performed …
Discovery of novel bacterial toxins by genomics and computational biology
Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin
identification begins with pathological studies of bacterial infectious disease. Following …
identification begins with pathological studies of bacterial infectious disease. Following …
Deep embedding and alignment of protein sequences
Protein sequence alignment is a key component of most bioinformatics pipelines to study the
structures and functions of proteins. Aligning highly divergent sequences remains, however …
structures and functions of proteins. Aligning highly divergent sequences remains, however …
An assessment of genome annotation coverage across the bacterial tree of life
B Lobb, BJM Tremblay… - Microbial …, 2020 - microbiologyresearch.org
Although gene-finding in bacterial genomes is relatively straightforward, the automated
assignment of gene function is still challenging, resulting in a vast quantity of hypothetical …
assignment of gene function is still challenging, resulting in a vast quantity of hypothetical …
A molecular portrait of de novo genes in yeasts
New genes, with novel protein functions, can evolve “from scratch” out of intergenic
sequences. These de novo genes can integrate the cell's genetic network and drive …
sequences. These de novo genes can integrate the cell's genetic network and drive …
Unifying the known and unknown microbial coding sequence space
Genes of unknown function are among the biggest challenges in molecular biology,
especially in microbial systems, where 40–60% of the predicted genes are unknown …
especially in microbial systems, where 40–60% of the predicted genes are unknown …
Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse
life forms on Earth. However, they have been discovered only 334 years ago, and their …
life forms on Earth. However, they have been discovered only 334 years ago, and their …
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
N Vakirlis, A Kupczok - Genome Research, 2024 - genome.cshlp.org
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In
prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in …
prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in …
Discovering novel hydrolases from hot environments
Novel hydrolases from hot and other extreme environments showing appropriate
performance and/or novel functionalities and new approaches for their systematic screening …
performance and/or novel functionalities and new approaches for their systematic screening …